RetrogeneDB ID: retro_mmus_147

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:69372793..69373321(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000044147
• Aliases: Arf6, AI788669, AW496366
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Arf3
• Ensembl ID: ENSMUSG00000051853
• Aliases: Arf3, 5430400P17Rik, AI854770
• Description: ADP-ribosylation factor 3 [Source:MGI Symbol;Acc:MGI:99432]

Sequence

>retro_mmus_147
ATGGGGAAGGTGCTATCCAAGATCTTCGGGAACAAGGAAATGCGGATCCTCATGCTGGGCCTGGACGCAGCCGGCAAGAC
AACGATCCTGTACAAGTTGAAGCTGGGCCAATCGGTGACCACCATCCCCACGGTGGGCTTCAACGTGGAGACGGTGACTT
ACAAAAACGTCAAGTTCAACGTGTGGGATGTGGGCGGCCAGGACAAGATCCGGCCGCTCTGGCGGCATTACTACACCGGG
ACCCAGGGTCTGATCTTCGTGGTAGACTGCGCCGACCGCGACCGCATCGACGAGGCCCGCCAGGAGCTGCACCGCATTAT
CAATGACCGGGAGATGAGGGACGCCATCATCCTCATCTTCGCCAACAAGCAGGACCTGCCCGATGCCATGAAACCCCATG
AGATCCAGGAGAAACTGGGCCTGACCCGGATTCGGGACAGGAACTGGTATGTGCAGCCCTCCTGTGCCACCTCCGGGGAC
GGACTCTATGAGGGGCTCACATGGTTAACCTCTAACTACAAATCCTAA

Alignment

ORF - retro_mmus_147 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.54 %
• Parental protein coverage: 96.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GNLLKSLIGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIR
          G..L....G.KEMRILM.GLDAAGKTTILYKLKLG..VTTIPT.GFNVETV.YKN..F.VWDVGGQDKIR
Retrocopy GKVLSKIFGNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIR

Parental  PLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGL
          PLWRHY...TQGLIFVVD..DR.R..EAR.EL.R.....E.RDA..L.FANKQDLP.AM...EI..KLGL
Retrocopy PLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGL

Parental  HSLRHRNWYIQATCATSGDGLYEGLDWLANQLKN
          ...R.RNWY.Q..CATSGDGLYEGL.WL....K.
Retrocopy TRIRDRNWYVQPSCATSGDGLYEGLTWLTSNYKS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	9.70 RPM	1302.01 RPM
SRP007412_cerebellum	9.86 RPM	497.61 RPM
SRP007412_heart	11.02 RPM	58.90 RPM
SRP007412_kidney	15.15 RPM	244.53 RPM
SRP007412_liver	15.40 RPM	102.00 RPM
SRP007412_testis	9.88 RPM	157.80 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_147 in 4 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	12:69371644..69373409
ENCFF001YIJ	POLR2A	12:69370873..69373493
ENCFF001YJZ	POLR2A	12:69370910..69372728
ENCFF001YKA	POLR2A	12:69370883..69373491

EST

No EST(s) were mapped for retro_mmus_147 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_24002	86 libraries	185 libraries	589 libraries	177 libraries	35 libraries

The graphical summary, for retro_mmus_147 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_147 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_147 has 12 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_36
Pan troglodytes	retro_ptro_5
Gorilla gorilla	retro_ggor_161
Pongo abelii	retro_pabe_126
Macaca mulatta	retro_mmul_174
Callithrix jacchus	retro_cjac_300
Rattus norvegicus	retro_rnor_272
Oryctolagus cuniculus	retro_ocun_132
Bos taurus	retro_btau_26
Sus scrofa	retro_sscr_82
Canis familiaris	retro_cfam_119
Equus caballus	retro_ecab_106

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008240	1 retrocopy	retro_acar_12,
Cavia porcellus	ENSCPOG00000025074	1 retrocopy	retro_cpor_92,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Homo sapiens	ENSG00000134287	1 retrocopy	retro_hsap_36,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Loxodonta africana	ENSLAFG00000004207	1 retrocopy	retro_lafr_115,
Macropus eugenii	ENSMEUG00000005072	7 retrocopies	retro_meug_1036, retro_meug_1117, retro_meug_1857, retro_meug_29, retro_meug_395, retro_meug_616, retro_meug_946,
Microcebus murinus	ENSMICG00000017545	1 retrocopy	retro_mmur_37,
Monodelphis domestica	ENSMODG00000013804	1 retrocopy	retro_mdom_241,
Mus musculus	ENSMUSG00000048076	1 retrocopy	retro_mmus_1718,
Mus musculus	ENSMUSG00000051853	1 retrocopy	retro_mmus_147 ,
Mus musculus	ENSMUSG00000062421	1 retrocopy	retro_mmus_2056,
Nomascus leucogenys	ENSNLEG00000017859	2 retrocopies	retro_nleu_1348, retro_nleu_94,
Petromyzon marinus	ENSPMAG00000000531	1 retrocopy	retro_pmar_5,
Rattus norvegicus	ENSRNOG00000033155	1 retrocopy	retro_rnor_272,
Rattus norvegicus	ENSRNOG00000048089	1 retrocopy	retro_rnor_2521,
Sarcophilus harrisii	ENSSHAG00000003635	2 retrocopies	retro_shar_25, retro_shar_364,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000004698	1 retrocopy	retro_ttru_1081,